SMTL ID : 8swa.1

Crystal structure of the human S-adenosylmethionine synthetase 1 in complex with SAM and PPNP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-dimer

Ligands

2 x PPK: (DIPHOSPHONO)AMINOPHOSPHONIC ACID(Non-covalent)

PPK.1: 16 residues within 4Å: Chain A: H.37, D.39, K.189, D.266, R.272, K.273 Chain B: D.142, G.287, G.288, A.289, K.293, D.299 Ligands: MG.2, MG.3, K.4, SAM.5 13 PLIP interactions: 4 interactions with chain B, 9 interactions with chain A Hydrogen bonds: B:D.142, B:A.289, B:K.293, B:D.299, A:D.266, A:D.266, A:R.272, A:R.272, A:K.273 Water bridges: A:K.189 Salt bridges: A:H.37, A:K.189, A:K.273 PPK.6: 16 residues within 4Å: Chain A: D.142, G.287, G.288, A.289, K.293, D.299 Chain B: H.37, D.39, K.189, D.266, R.272, K.273 Ligands: MG.7, MG.8, K.9, SAM.10 13 PLIP interactions: 4 interactions with chain A, 9 interactions with chain B Hydrogen bonds: A:D.142, A:A.289, A:K.293, A:D.299, B:D.266, B:D.266, B:R.272, B:R.272, B:K.273 Water bridges: B:K.189 Salt bridges: B:H.37, B:K.189, B:K.273

4 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain A: D.39, K.273 Ligands: PPK.1, K.4 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.39, H2O.2, H2O.2 MG.3: 2 residues within 4Å: Chain B: D.299 Ligands: PPK.1 3 PLIP interactions: 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.299, H2O.3, H2O.10 MG.7: 4 residues within 4Å: Chain B: D.39, K.273 Ligands: PPK.6, K.9 3 PLIP interactions: 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.39, H2O.11, H2O.11 MG.8: 2 residues within 4Å: Chain A: D.299 Ligands: PPK.6 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.299, H2O.1, H2O.12

2 x K: POTASSIUM ION(Non-covalent)

K.4: 5 residues within 4Å: Chain A: D.266, A.267 Chain B: E.65 Ligands: PPK.1, MG.2 4 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: B:E.65, A:D.266, A:A.267, H2O.10 K.9: 5 residues within 4Å: Chain A: E.65 Chain B: D.266, A.267 Ligands: PPK.6, MG.7 4 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: B:D.266, B:A.267, A:E.65, H2O.1

2 x SAM: S-ADENOSYLMETHIONINE(Non-covalent)

SAM.5: 20 residues within 4Å: Chain A: H.37, P.38, D.187, K.189, S.214, S.255, R.257, F.258, I.260, D.266 Chain B: A.63, E.78, Q.121, D.124, I.125, G.141, D.142, K.297, I.330 Ligands: PPK.1 18 PLIP interactions: 11 interactions with chain A, 7 interactions with chain B Hydrogen bonds: A:D.187, A:S.255, A:R.257, A:D.266, A:D.266, B:E.78, B:Q.121 Water bridges: A:S.214, A:S.255, A:A.267, B:K.297, B:K.297, B:K.297 Salt bridges: A:D.266, B:D.142, B:K.297 pi-Stacking: A:F.258, A:F.258 SAM.10: 20 residues within 4Å: Chain A: A.63, E.78, Q.121, D.124, I.125, G.141, D.142, K.297, I.330 Chain B: H.37, P.38, D.187, K.189, S.214, S.255, R.257, F.258, I.260, D.266 Ligands: PPK.6 18 PLIP interactions: 11 interactions with chain B, 7 interactions with chain A Hydrogen bonds: B:D.187, B:S.255, B:R.257, B:D.266, B:D.266, A:E.78, A:Q.121 Water bridges: B:S.214, B:S.255, B:A.267, A:K.297, A:K.297, A:K.297 Salt bridges: B:D.266, A:D.142, A:K.297 pi-Stacking: B:F.258, B:F.258

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Pham, V.N. et al., Formaldehyde regulates S -adenosylmethionine biosynthesis and one-carbon metabolism. Science (2023)

Release Date

2023-11-15

Peptides

S-adenosylmethionine synthase isoform type-1: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

S-adenosylmethionine synthase isoform type-1